R01 GM123511 Richard Young Proper control of gene expression programs is fundamental to cellular health and its dysregulation has been implicated in many human diseases. The gene expression programs of mammalian cells are regulated by diverse transcription factors and cofactors, which occupy specific genomic loci and cause RNA polymerase II to transcribe specific genes. When regulated properly, this transcriptional circuitry produces healthy cells, but many inherited and infectious diseases cause cells to have dysregulated gene expression programs. While pursuing the original aims of our project, we discovered that components of the transcription apparatus form a liquid-like condensate that compartmentalizes and concentrates these transcriptional molecules at super-enhancers and their associated genes (Cell 2018, PMC6295254, Science, 2018, PMC6092193; Nature 2019, PMC6706314). This new model has led us to fundamental new insights; for example, the heretofore mysterious activation domains of transcription factors, whose intrinsically disordered domains do not form stable structures amenable to crystallography, are now understood to activate genes through their ability to form dynamic condensates with coactivators and RNA polymerase II. Gaps in our knowledge of the factors that contribute to transcriptional condensates now limit our understanding of the mechanisms by which these factors contribute to specific cell states in health and disease. The new condensate model for transcriptional control, and recent evidence that SARS-CoV-2 modulates host cell gene expression by sequestering host components that normally occur in nuclear condensates, compels us to pursue simultaneously both our original goal of improving our understanding of human gene control and a new goal of deciphering how SARS-CoV-2 alters normal host cell gene expression. To accomplish this goals, the specific aims of the project are: 1) identify and characterize the functions of coactivators in active transcriptional condensates, 2) identify and characterize the functions of corepressors in heterochromatic condensates, and 3) determine how host cell gene expression is manipulated by SARS-CoV-2 accessory proteins, which have been shown to bind and sequester host cell transcriptional coactivators and corepressors. These related studies promise to continue to produce new insights into the control of gene expression programs and should generate new insights into the mechanisms by which SARS-CoV-2 alters these programs, thereby providing clues to mechanisms with potential therapeutic value.